Yes that's because it's not flagged transparent in the code. Minecraft does this thing called culling, in which the game will only render surfaces that you can see (ie surfaces that have a form of transparent block next to them, such as air, glass, a bed, chest, fence, etc). This is done to decrease the work your GPU has to do and thus make the game run faster, however it causes things like this.
The model itself is transparent, but in the code it has to be flagged as transparent which the crafting table is not. Unfortunately you cannot stop this from happening unless you make a mod to flag the crafting table as transparent.
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Author of the Clarity, Serenity, Sapphire & Halcyon shader packs for Minecraft: Java Edition.